I made the trip a few years ago from SF to San Jose via Caltrain then on the ACE to Stockton on the first PM ACE train out of San Jose around 4 pm, then took a San Joaquin back to Emeryville and Amtrak bus back to SF ... There was a city bus from the old SP station used by ACE to the Santa Fe station used by the San Joaquin to get back to the Bay Area. It is a long walk from ACE to the Santa Fe station. Viewed from the bus, the route didn't seem to be too bad but there's no need to walk The city bus stopped right at the Santa Fe station. Area south of the station is residential may not be safe but there's no need to go south of the station. I don't know about that area but it was fine in the daytime around the station waiting for the Westbound San Joaquin that arrived around 6 pm. I believe the Santa Fe station had a sign prohibiting overnight parking. The area may be more dangerous after dark. In the spring and summertime with daylight savings time it should be OK to do the eastbound trip out of San Jose on the first PM train if the mid day one is discontinued and return on the San Joaquin as I did.